From 3935e9bee66fbfff4f35365eb9cff8c79f5fadd8 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 29 Oct 2015 10:09:13 +0000
Subject: patch merge

---
 views/batch.haml     | 3 +--
 views/neighbors.haml | 4 ++--
 views/predict.haml   | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index 8389651..ec987c4 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -44,7 +44,7 @@
                 %br
                 %b Prediction:
                 / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
@@ -53,4 +53,3 @@
               - else
                 %p
                   = "Not enough similar compounds </br>in training dataset."
-              %p
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 21b4b35..a741b45 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -58,7 +58,7 @@
                     / %td
                 %tbody
                   - type = @model_types[j]
-                - prediction[:neighbors].each_with_index do |neighbor,count|
+                - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
@@ -67,7 +67,7 @@
                       %p= Compound.find(neighbor[0]).smiles
                     / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join(", ") : neighbor[2].join(", ")
+                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/predict.haml b/views/predict.haml
index 9863cd9..8ab9ee0 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -24,7 +24,7 @@
   });  
   
   function getInput(){
-    identifier = document.getElementById("identifier").value;
+    identifier = document.getElementById("identifier").value.trim();
     fileselect = document.getElementById("fileselect").value;
     if (fileselect != ""){
       return 1;
-- 
cgit v1.2.3


From 1d6588b35b4ffff16717e24b42a0d396d5347f95 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 26 Jan 2016 12:53:40 +0000
Subject: batch merge

---
 views/batch.haml      | 15 +++++++++------
 views/neighbors.haml  | 21 ++++++++++++++++++---
 views/predict.haml    |  1 -
 views/prediction.haml | 14 +++++++++-----
 4 files changed, 36 insertions(+), 15 deletions(-)

(limited to 'views')

diff --git a/views/batch.haml b/views/batch.haml
index ec987c4..9bfa67e 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -18,6 +18,7 @@
       / key = compound, values = array of arrays with model, prediction
       - @batch.each do |key, values|
         - compound = key
+        - mw = compound.molecular_weight
         %tr
           %td{:style=>"vertical-align:top;"}
             %p= compound.svg
@@ -32,10 +33,13 @@
               %p
               - if prediction[:confidence] == "measured"
                 %p
-                / TODO fix scientific notation from database
-                %b Measured activity:
-                = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
-                %p Compound is part of the training dataset
+                  %b Measured activity:
+                - if prediction[:value].is_a?(Array)
+                  = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %p 
+                %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -43,8 +47,7 @@
                 = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index a741b45..6001605 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -29,7 +29,20 @@
                 debug: false,
                 theme: "bootstrap",
                 headerTemplate: '{content} {icon}',
-                widgets: ['zebra', 'columns', 'uitheme'],
+                widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'],
+                widgetOptions: {
+                  stickyHeaders_attachTo : '.tab-content',
+                  stickyHeaders : '',
+                  stickyHeaders_offset : 0,
+                  stickyHeaders_cloneId : '-sticky',
+                  stickyHeaders_addResizeEvent : true,
+                  stickyHeaders_includeCaption : true,
+                  stickyHeaders_zIndex : 2,
+                  stickyHeaders_attachTo : null,
+                  stickyHeaders_xScroll : null,
+                  stickyHeaders_yScroll : null,
+                  stickyHeaders_filteredToTop: true
+                },
                 headers: {0: {sorter: false}, 3: {sorter: false}},
                 sortList: [[2,1]],
                 widthFixed: false
@@ -65,9 +78,11 @@
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= Compound.find(neighbor[0]).svg
                       %p= Compound.find(neighbor[0]).smiles
+                    - c = Compound.find(neighbor[0])
+                    //- mw = c.molecular_weight
                     / Measured Activity
-                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
+                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
+                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/predict.haml b/views/predict.haml
index 8ab9ee0..010ed12 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,7 +125,6 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      // disable for public version
       %label{:for=>"fileselect"}
         or upload a CSV file for batch predictions (disabled in public version)
       %br
diff --git a/views/prediction.haml b/views/prediction.haml
index ef0c5db..33e9ec5 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,6 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
+          -#- mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -30,10 +31,14 @@
               - if prediction[:confidence] == "measured"
                 - @dbhit[i] = true
                 %p
-                / TODO fix scientific notation from database
                 %b Measured activity:
-                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
-                %p Compound is part of the training dataset
+                - p prediction[:value]
+                - if prediction[:value].is_a?(Array)
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
+                %p
+                  %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -41,8 +46,7 @@
                 = type
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
                 / TODO update description
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
-- 
cgit v1.2.3


From 9eb9fd8ab470d6c44c70e0af0808204bdda2b161 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 17 Mar 2016 11:28:18 +0000
Subject: snapshot, works only with png plots

---
 views/model_details.haml | 24 ++++++++++++------------
 views/style.scss         |  9 +++++++++
 2 files changed, 21 insertions(+), 12 deletions(-)

(limited to 'views')

diff --git a/views/model_details.haml b/views/model_details.haml
index e5886e7..04cc0f0 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -97,10 +97,9 @@ Source:
                 -#= "Confusion Matrix:\t"
                 -#= cv.confusion_matrix
         %br
-        -#%p
-          = "Confidence plot:"
-        -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;padding:0;"}
-          = cv.confidence_plot
+        = "Confidence plot:"
+        %p.plot
+          %img{:src=>"confp#{cv.id}.png"}
       - if model.regression?
         %br
         = "Root mean squared error:\t"
@@ -117,12 +116,13 @@ Source:
         %br 
         = "R square:\t"
         = cv.r_squared.round(3) if cv.r_squared
-        -#%p
-          = "Correlation plot"
-        -#%p{:id=>"corrp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"}
-          =cv.correlation_plot
-        -#%p
-          = "Confidence plot:"
-        -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"}
-          = cv.confidence_plot
+        %br
+        = "Confidence plot:"
+        %p.plot
+          %img{:src=>"/confp#{cv.id}.png"}
+        %br
+        = "Correlation plot"
+        %p.plot
+          %img{:src=>"/corrp#{cv.id}.png"}
+        
 %br
diff --git a/views/style.scss b/views/style.scss
index 9a3c9df..a0502b5 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -16,3 +16,12 @@ h4.head-back, h5.head-back{
     height: 5em;
   }
 }
+img {
+  max-width: 100%;
+  max-height: 100%;
+}
+
+.plot {
+  height: 300px;
+  width: 300px;
+}
-- 
cgit v1.2.3


From 510822b13d48344ffe4e047a4415ebdb218dadc0 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 24 Mar 2016 19:41:37 +0000
Subject: updated for latest lazar changes; introduced 95% prediction interval

---
 views/model_details.haml | 29 ++++++++++-------------------
 views/neighbors.haml     | 31 +++++++++++++++++++++----------
 views/prediction.haml    | 11 ++++++++---
 3 files changed, 39 insertions(+), 32 deletions(-)

(limited to 'views')

diff --git a/views/model_details.haml b/views/model_details.haml
index 04cc0f0..34e86ac 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -36,9 +36,6 @@ Source:
         = "Accuracy:\t"
         = cv.accuracy.round(3) if cv.accuracy
         %br
-        = "Weighted Accuracy:\t"
-        = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
-        %br
         = "True positive rate:\t"
         = cv.true_rate["active"].round(3) if cv.true_rate["active"]
         %br
@@ -97,32 +94,26 @@ Source:
                 -#= "Confusion Matrix:\t"
                 -#= cv.confusion_matrix
         %br
-        = "Confidence plot:"
-        %p.plot
-          %img{:src=>"confp#{cv.id}.png"}
+        /= "Confidence plot:"
+        /%p.plot
+        /  %img{:src=>"confp#{cv.id}.svg"}
       - if model.regression?
         %br
         = "Root mean squared error:\t"
         = cv.rmse.round(3) if cv.rmse
         %br
-        = "Weighted root mean squared error:\t"
-        = cv.weighted_rmse.round(3) if cv.weighted_rmse
-        %br
         = "Mean absolute error:\t"
         = cv.mae.round(3) if cv.mae
-        %br
-        = "Weighted mean absolute error:\t"
-        = cv.weighted_mae.round(3) if cv.weighted_mae
         %br 
         = "R square:\t"
         = cv.r_squared.round(3) if cv.r_squared
         %br
-        = "Confidence plot:"
-        %p.plot
-          %img{:src=>"/confp#{cv.id}.png"}
-        %br
-        = "Correlation plot"
-        %p.plot
-          %img{:src=>"/corrp#{cv.id}.png"}
+        /= "Confidence plot:"
+        /%p.plot
+        /  %img{:src=>"/confp#{cv.id}.svg"}
+        /%br
+        /= "Correlation plot"
+        /%p.plot
+        /  %img{:src=>"/corrp#{cv.id}.svg"}
         
 %br
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 6001605..6011a6d 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -9,7 +9,17 @@
   #tabs
     %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
       / each model a tab head ;
+      / hash for predictionFeature
+      - predictionFeature = {}
       - @models.each_with_index do |model,i|
+        / get predictionFeature type
+        - m = Model::Lazar.find model.model_id.to_s
+        - predFeature = Feature.find m.prediction_feature_id.to_s
+        / define feature type (numeric : nominal)
+        - predFeatureType = (predFeature.numeric? ? "numeric" : "nominal")
+        / use prediction feature id for neighbor compound features
+        - predFeatureId = m.prediction_feature_id.to_s
+        - predictionFeature[i] = {"id" => predFeatureId, "type" => predFeatureType}
         %li{:class => ("active" if i == 0)}
           %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}}
             = "#{model.endpoint} (#{model.species})"
@@ -29,7 +39,7 @@
                 debug: false,
                 theme: "bootstrap",
                 headerTemplate: '{content} {icon}',
-                widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'],
+                widgets: ['columns', 'uitheme', 'stickyHeaders'],
                 widgetOptions: {
                   stickyHeaders_attachTo : '.tab-content',
                   stickyHeaders : '',
@@ -74,19 +84,20 @@
                 - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
+                    - c = Compound.find(neighbor["_id"])
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
-                      /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
-                      %p= Compound.find(neighbor[0]).svg
-                      %p= Compound.find(neighbor[0]).smiles
-                    - c = Compound.find(neighbor[0])
-                    //- mw = c.molecular_weight
-                    / Measured Activity
+                      /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
+                      %p= c.svg
+                      %p= c.smiles
+                    - mw = c.molecular_weight
+                    / Measured Activity = compound.features
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
-                    / Similarity
+                      - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
+                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : features.join("</br>")
+                    / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-                      = neighbor[1] != nil ? neighbor[1].round(2) : "Not enough similar compounds </br>in training dataset."
+                      = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset."
 
           - else
             %span.btn.btn-default.disabled
diff --git a/views/prediction.haml b/views/prediction.haml
index 33e9ec5..aeaafdc 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          -#- mw = @compound.molecular_weight
+          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -51,8 +51,13 @@
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
                 / TODO probability
-                %b Confidence:
-                = prediction[:confidence].round(2)
+                - if type == "Regression"
+                  %b 95% Prediction interval:
+                  - interval = prediction[:prediction_interval].collect{|i| i.round(2)}
+                  = interval
+                - else
+                  %b Confidence:
+                  = prediction[:confidence].round(2) unless prediction[:confidence].nil?
                 / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
                 %p
                 /TODO add tooltip for significant ftagments and descriptors
-- 
cgit v1.2.3


From d70373fb5a35740f1246d9a37ce1567e899c8a1a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 31 Mar 2016 10:53:45 +0200
Subject: catch empty pred interval

---
 views/prediction.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/prediction.haml b/views/prediction.haml
index aeaafdc..f99df75 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -53,7 +53,7 @@
                 / TODO probability
                 - if type == "Regression"
                   %b 95% Prediction interval:
-                  - interval = prediction[:prediction_interval].collect{|i| i.round(2)}
+                  - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)}
                   = interval
                 - else
                   %b Confidence:
-- 
cgit v1.2.3


From df8ed98fcc052da2641c26897a8dd0592f274e53 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Fri, 15 Apr 2016 09:59:43 +0000
Subject: reactivated info buttons; changed unit for fish; introduced FAQ

---
 views/faq.haml        |  2 ++
 views/faq_layout.haml | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++
 views/layout.haml     |  5 +++-
 views/neighbors.haml  |  7 +++---
 views/prediction.haml | 23 ++++++++++--------
 views/style.scss      | 12 +++++++++
 6 files changed, 102 insertions(+), 14 deletions(-)
 create mode 100644 views/faq.haml
 create mode 100644 views/faq_layout.haml

(limited to 'views')

diff --git a/views/faq.haml b/views/faq.haml
new file mode 100644
index 0000000..818b96a
--- /dev/null
+++ b/views/faq.haml
@@ -0,0 +1,2 @@
+%div.well.faq
+  = @faq
diff --git a/views/faq_layout.haml b/views/faq_layout.haml
new file mode 100644
index 0000000..a9b6664
--- /dev/null
+++ b/views/faq_layout.haml
@@ -0,0 +1,67 @@
+!!!
+%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
+  %head
+    %meta{'charset'=>"utf-8"}
+    %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
+    %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
+    %title Lazar GUI FAQ
+    %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
+    %link{ :href=>"/style.css", :rel=>"stylesheet"}
+    %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"}
+    %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
+    %script{:src=>"/javascripts/bootstrap.min.js"}
+    %script{ :src=>"/javascripts/lazar-gui.js"}
+  %body
+    %noscript
+      %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
+      Your web browser must have JavaScript enabled in order for this application to display correctly.
+    %header.page-header
+      %div.row
+        %div.col-md-2
+          %a{:href=> to("/predict")}
+            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
+        %div.col-md-10
+          %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI
+          A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework
+    
+    %div.container-fluid
+      :javascript
+        $(document).ready(function(){
+          $("#back-top").hide();
+          $(".blind").error(function(){
+            $(this).attr('src', '/images/blind.png');
+          });
+        });
+          
+      = yield
+    
+    %footer.footer
+      %div.container-fluid
+        %p.text-muted
+          &copy; 
+          %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+
+    #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
+      %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
+        %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"}
+    :javascript
+      $("#back-top").hide();
+      $(function () {
+        $(window).scroll(function () {
+          if ($(this).scrollTop() > 600) {
+            $('#back-top').fadeIn();
+          } else {
+            $('#back-top').fadeOut();
+          }
+        });
+        // scroll body to 0px on click
+        $('#back-top a').click(function () {
+          $('body,html').animate({
+            scrollTop: 0
+          }, 500);
+          return false;
+        });
+      });
diff --git a/views/layout.haml b/views/layout.haml
index 60f2bb3..46d326d 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -16,7 +16,7 @@
     %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
     %script{ :src=>"/javascripts/lazar-gui.js"}
-  %body{:style=>"background-color:#E7E7E7"}
+  %body
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
       Your web browser must have JavaScript enabled in order for this application to display correctly.
@@ -27,6 +27,9 @@
             %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
           %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions
+        %div.col-md-2
+          %a.btn.btn-info{:href=> to("/faq"), :rel => "external"}
+            FAQ
     
     %div.container-fluid
       :javascript
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 6011a6d..c94331a 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -75,12 +75,13 @@
                   %tr
                     %td
                     %td{:style=>"font-size:x-small;padding:0px;"}
-                      / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %td{:style=>"font-size:x-small;padding:0px;"}
-                      / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"}
                     / %td
                 %tbody
                   - type = @model_types[j]
+                  - unit = @models[j].unit
                 - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
@@ -93,7 +94,7 @@
                     / Measured Activity = compound.features
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
                       - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
-                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : features.join("</br>")
+                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" | #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/prediction.haml b/views/prediction.haml
index f99df75..89c33d6 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -24,6 +24,7 @@
           - @predictions.each_with_index do |prediction,i|
             - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression"
             - @model_types[i] = type
+            - unit = @models[i].unit
             %td{:style=>"vertical-align:top;white-space:nowrap;"}
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
@@ -34,9 +35,9 @@
                 %b Measured activity:
                 - p prediction[:value]
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+"|#{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 %p
                   %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
@@ -46,27 +47,29 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
-                / TODO update description
-                / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
-                / TODO probability
                 - if type == "Regression"
                   %b 95% Prediction interval:
                   - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)}
-                  = interval
+                  = "[#{interval[0]} (#{unit}), #{interval[1]} (#{unit})]"
+                  / prediction intervall popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"A <b>prediction interval</b> (<a href='https://en.wikipedia.org/wiki/Prediction_interval', target='_blank'>wikipedia</a>) is an estimate of an interval in which future observations will fall, with a certain probability, given what has already been observed."}}
                 - else
                   %b Confidence:
                   = prediction[:confidence].round(2) unless prediction[:confidence].nil?
-                / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
+                  / confidence popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
                 %p
                 /TODO add tooltip for significant ftagments and descriptors
                 / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
                 / Significant fragments:
-                / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
+                / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
                 / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
                 / Descriptors
-                / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
+                / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
                 / %p
                 %p
               - else
diff --git a/views/style.scss b/views/style.scss
index a0502b5..70c8035 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -1,3 +1,6 @@
+body {
+  background-color:#E7E7E7;
+}
 table.table-borderless tbody tr td{
   border-top: none;
 }
@@ -25,3 +28,12 @@ img {
   height: 300px;
   width: 300px;
 }
+.faq {
+  text-align: block;
+  margin-left:15%;
+  margin-right:15%;
+  margin-top:2%;
+}
+.faq h1 {
+  text-align: center;
+}
-- 
cgit v1.2.3


From 512458e2489c8cc12a9d539d8895c1802d7b081a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 20 Apr 2016 14:12:03 +0000
Subject: adopted changes from CH on the master branch

---
 views/neighbors.haml  | 4 +++-
 views/prediction.haml | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/neighbors.haml b/views/neighbors.haml
index c94331a..3014255 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -75,9 +75,11 @@
                   %tr
                     %td
                     %td{:style=>"font-size:x-small;padding:0px;"}
+                      / measured activity
                       %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %td{:style=>"font-size:x-small;padding:0px;"}
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"}
+                      / similarity
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/Molprint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %td
                 %tbody
                   - type = @model_types[j]
diff --git a/views/prediction.haml b/views/prediction.haml
index 89c33d6..4a2877e 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -49,6 +49,7 @@
                 %b Prediction:
                 = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
+                / prediction popover
                 %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
                 - if type == "Regression"
-- 
cgit v1.2.3


From 5c40dfe6ca17d318a0ec0dfcfe07b174f4d71e59 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 20 Apr 2016 14:19:02 +0000
Subject: edited model details

---
 views/model_details.haml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'views')

diff --git a/views/model_details.haml b/views/model_details.haml
index 34e86ac..1be75e7 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -4,21 +4,19 @@ Source:
 %a{:href=>model.source, :target=>"external"}
   = model.source
 %br
-= "Algorithm:\tLAZAR"
-%br
 - model.classification? ? type = "Classification" : type = "Regression"
 = "Type:\t"
 = type
 %br
 - training_dataset = OpenTox::Dataset.find model.training_dataset.id
-= "Training dataset:\t"
-= training_dataset.source.split("/").last
-%br
 = "Training compounds:\t"
 = training_dataset.compounds.size
 
 %p
-%b Crossvalidation (3 independent):
+- if type == "Classification"
+  %b Independent crossvalidations:
+- else
+  %b Independent crossvalidations (-log10 transformed):
 %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"}
   - model.crossvalidations.each do |crossvalidation|
     %span.col-xs-4.col-sm-4.col-md-4.col-lg-4
-- 
cgit v1.2.3


From 7759519665408673e2ab1bfd8d32a84168c2ee34 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 20 Apr 2016 14:39:22 +0000
Subject: adjusted prediction intervall info; units ; depiction

---
 views/prediction.haml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'views')

diff --git a/views/prediction.haml b/views/prediction.haml
index 4a2877e..5265504 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -47,7 +47,7 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
                 %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
@@ -55,9 +55,10 @@
                 - if type == "Regression"
                   %b 95% Prediction interval:
                   - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)}
-                  = "[#{interval[0]} (#{unit}), #{interval[1]} (#{unit})]"
+                  %br
+                  = "[#{interval[0]} - #{interval[1]}] (#{unit}), [#{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])}] (mg/L)"
                   / prediction intervall popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"A <b>prediction interval</b> (<a href='https://en.wikipedia.org/wiki/Prediction_interval', target='_blank'>wikipedia</a>) is an estimate of an interval in which future observations will fall, with a certain probability, given what has already been observed."}}
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                 - else
                   %b Confidence:
                   = prediction[:confidence].round(2) unless prediction[:confidence].nil?
-- 
cgit v1.2.3


From 48738e50ab34768cccfc770d3010c4f055bd76eb Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 20 Apr 2016 14:44:57 +0000
Subject: updated similarity info; changed delimiter

---
 views/neighbors.haml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'views')

diff --git a/views/neighbors.haml b/views/neighbors.haml
index 3014255..2edc3ab 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -79,7 +79,7 @@
                       %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
                     %td{:style=>"font-size:x-small;padding:0px;"}
                       / similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/Molprint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %td
                 %tbody
                   - type = @model_types[j]
@@ -96,7 +96,7 @@
                     / Measured Activity = compound.features
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
                       - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
-                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" | #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
+                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-- 
cgit v1.2.3


From 9d6043aef3836e0678942dccda2d8eeda0dc17b4 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 20 Apr 2016 14:49:21 +0000
Subject: keep back faq

---
 views/layout.haml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 46d326d..a49238f 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -27,9 +27,9 @@
             %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
           %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions
-        %div.col-md-2
-          %a.btn.btn-info{:href=> to("/faq"), :rel => "external"}
-            FAQ
+        /%div.col-md-2
+        /  %a.btn.btn-info{:href=> to("/faq"), :rel => "external"}
+        /    FAQ
     
     %div.container-fluid
       :javascript
-- 
cgit v1.2.3


From b8d1ce9a588534e1a92bd4461c94b97b6269291c Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 21 Apr 2016 08:18:51 +0000
Subject: removed brackets

---
 views/prediction.haml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'views')

diff --git a/views/prediction.haml b/views/prediction.haml
index 5265504..d8312bb 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -50,13 +50,13 @@
                 = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Lazar calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. Lazar calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
                 %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
-                  - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)}
+                  - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)}
                   %br
-                  = "[#{interval[0]} - #{interval[1]}] (#{unit}), [#{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])}] (mg/L)"
+                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} (mg/L)"
                   / prediction intervall popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                 - else
-- 
cgit v1.2.3


From 1a09ee962a769dfe2ef49dcd6fb865381c221788 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 21 Apr 2016 10:29:52 +0000
Subject: updated prediction info

---
 views/prediction.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'views')

diff --git a/views/prediction.haml b/views/prediction.haml
index d8312bb..709e17e 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -50,7 +50,7 @@
                 = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Lazar calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. Lazar calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>Lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                 %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
-- 
cgit v1.2.3


From b3fffd49c61745e953415c50084fee900d8029e9 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 21 Apr 2016 13:45:20 +0000
Subject: fixed neighbors table; bg-color predictions due to safari; disabled
 neighbors sort option; enabled table header info icons

---
 views/layout.haml     | 17 +++++++++--------
 views/neighbors.haml  | 24 ++++++++----------------
 views/prediction.haml | 10 +++++-----
 views/style.scss      |  4 ++++
 4 files changed, 26 insertions(+), 29 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index a49238f..1220cf5 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -4,7 +4,7 @@
     %meta{'charset'=>"utf-8"}
     %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
     %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
-    %title Lazar Toxicity Predictions
+    %title lazar Toxicity Predictions
     %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
     %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
     %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
@@ -20,17 +20,18 @@
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
       Your web browser must have JavaScript enabled in order for this application to display correctly.
-    %header.page-header
+    %header.page-header{:style=>"margin:20px 0 20px;text-align:justify;display:inline-block;width:100%;"}
       %div.row
         %div.col-md-2
           %a{:href=> to("/predict")}
-            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
+            %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
-          %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions
-        /%div.col-md-2
-        /  %a.btn.btn-info{:href=> to("/faq"), :rel => "external"}
-        /    FAQ
-    
+          %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
+            lazar Toxicity Predictions
+        %div.col-md-2
+          %h1.media-heading{:style=>"margin: 0 0 0 1em;"}
+            %small
+              %a{:href=>"https://nano-lazar.in-silico.ch/predict"} nano-lazar
     %div.container-fluid
       :javascript
         $(document).ready(function(){
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 2edc3ab..096e432 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -38,7 +38,7 @@
               $("table##{j+1}").tablesorter({
                 debug: false,
                 theme: "bootstrap",
-                headerTemplate: '{content} {icon}',
+                headerTemplate: '',
                 widgets: ['columns', 'uitheme', 'stickyHeaders'],
                 widgetOptions: {
                   stickyHeaders_attachTo : '.tab-content',
@@ -53,34 +53,26 @@
                   stickyHeaders_yScroll : null,
                   stickyHeaders_filteredToTop: true
                 },
-                headers: {0: {sorter: false}, 3: {sorter: false}},
                 sortList: [[2,1]],
+                headers: {sorter: false},
                 widthFixed: false
               });
             });
           - if prediction[:neighbors].size > 0
             %div.table-responsive
-              %table.tablesorter{:id=>"#{j+1}", :style=>"border-style: solid;"}
+              %table{:id=>"#{j+1}", :style=>"border-style: solid;"}
                 %thead
                   %tr
-                    %th{:style =>"vertical-align:middle;"}
+                    %th.sorter-false{:style =>"vertical-align:middle;"}
                       Compound
-                    %th{:style =>"vertical-align:middle;"}
+                    %th.sorter-false{:style =>"vertical-align:middle;"}
                       Measured Activity
-                    %th{:style =>"vertical-align:middle;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                    %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
                     / %th{:style =>"vertical-align:middle;"}
                     / Supporting Information
-                %span
-                  %tr
-                    %td
-                    %td{:style=>"font-size:x-small;padding:0px;"}
-                      / measured activity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
-                    %td{:style=>"font-size:x-small;padding:0px;"}
-                      / similarity
-                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
-                    / %td
                 %tbody
                   - type = @model_types[j]
                   - unit = @models[j].unit
diff --git a/views/prediction.haml b/views/prediction.haml
index 709e17e..0f3d57b 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -12,7 +12,7 @@
   / displays all prediction result in first table
   %h3 Prediction Results:
   %div.table-responsive
-    %table.table.table-bordered{:id=>"overview", :style=>"background-color:white;"}
+    %table.table.table-bordered{:id=>"overview"}
       %tbody
         %tr
           %td{:id=>"compound", :style=>"vertical-align:top;"}
@@ -35,9 +35,9 @@
                 %b Measured activity:
                 - p prediction[:value]
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+"|#{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 %p
                   %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
@@ -50,13 +50,13 @@
                 = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
-                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>Lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                 %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
                   - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)}
                   %br
-                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} (mg/L)"
+                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"
                   / prediction intervall popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
                 - else
diff --git a/views/style.scss b/views/style.scss
index 70c8035..29f532b 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -37,3 +37,7 @@ img {
 .faq h1 {
   text-align: center;
 }
+.tablesorter-bootstrap thead .sorter-false {
+  cursor: default;
+}
+
-- 
cgit v1.2.3


From feb1a1cef0d750d009e72914345dc4bf2bd625ba Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 25 Apr 2016 16:01:07 +0000
Subject: added links;share;acknowledgements

---
 views/layout.haml | 53 +++++++++++++++++++++++++++++++++++++++++++++++------
 views/style.scss  | 27 ++++++++++++++++++++++++++-
 2 files changed, 73 insertions(+), 7 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 1220cf5..09968e9 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -20,7 +20,7 @@
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
       Your web browser must have JavaScript enabled in order for this application to display correctly.
-    %header.page-header{:style=>"margin:20px 0 20px;text-align:justify;display:inline-block;width:100%;"}
+    %header.page-header
       %div.row
         %div.col-md-2
           %a{:href=> to("/predict")}
@@ -29,10 +29,14 @@
           %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
             lazar Toxicity Predictions
         %div.col-md-2
-          %h1.media-heading{:style=>"margin: 0 0 0 1em;"}
+          %h1.media-heading
             %small
-              %a{:href=>"https://nano-lazar.in-silico.ch/predict"} nano-lazar
+              %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar
+          %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version
+
     %div.container-fluid
+      Problems, bugs, ideas for improvements ? Please report at our
+      %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -40,14 +44,51 @@
             $(this).attr('src', '/images/blind.png');
           });
         });
+        $(document).ready(function(){
+          $('[data-toggle="popover"]').popover();
+          $('.modal').on('hidden.bs.modal', function () {
+            $(this).removeData('bs.modal');
+          });
+        });
           
       = yield
     
     %footer.footer
       %div.container-fluid
-        %p.text-muted
-          &copy; 
-          %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+        %div.row
+          %div.col-md-8
+            %p.text-muted
+              &copy; 
+              %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+          %div.col-md-4
+            %button.btn.btn-default{:type=>"button", :data=>{:toggle=>"modal", :target=>"#acknowledgements"}} acknowledgements
+            %div.modal.fade{:id=>"acknowledgements", :role=>"dialog"}
+              %div.modal-dialog
+                %div.modal-content
+                  %div.modal-header
+                    %button{:type=>"button", :class=>"close", :data=>{:dismiss=>"modal"}}
+                      &times;
+                    %h4.modal-title Financial support:
+                  %div.modal-body
+                    %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
+                      %img{:src=>"/images/bfr_logo.gif"}
+                    %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
+                      %img{:src=>"/images/ot_logo.png"}
+                    %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
+                      %img{:src=>"/images/enm_logo.png"}
+    
+            %div.btn-group.dropup
+              %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share
+              %ul.dropdown-menu{:class=>"share-buttons"}
+                %li
+                  %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
+                    %img{:src=>"/images/Twitter.png"}
+                %li
+                  %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
+                    %img{:src=>"/images/Google+.png"}
+                %li
+                  %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
+                    %img{:src=>"/images/LinkedIn.png"}
 
     #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
       %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
diff --git a/views/style.scss b/views/style.scss
index 29f532b..77c7c4e 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -40,4 +40,29 @@ img {
 .tablesorter-bootstrap thead .sorter-false {
   cursor: default;
 }
-
+ul.share-buttons{
+  list-style: none;
+}
+.dropdown-menu {
+  min-width: 0px !important;
+  width:60px;
+}
+.dropdown-menu a {
+  padding: 0 2px 1px 2px !important;
+}
+.page-header{
+  margin:20px 0 20px;
+  text-align:justify;
+  display:inline-block;
+  width:98.5%;
+}
+.footer .modal img{
+  width: 250px;
+  padding: 1em;
+}
+footer button{
+  padding-bottom: 1em !important;
+}
+.dropdown-menu img{
+  margin-left: 0.7em;
+}
-- 
cgit v1.2.3


From 6c330fdcdf4ac941b0dab1aeb1add75bb5c4eae2 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 25 Apr 2016 16:09:59 +0000
Subject: added content to acknowledgement

---
 views/layout.haml | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 09968e9..5965ee1 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -76,6 +76,8 @@
                       %img{:src=>"/images/ot_logo.png"}
                     %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
                       %img{:src=>"/images/enm_logo.png"}
+                    %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
+                      %img{:src=>"/images/nestec.jpg"}
     
             %div.btn-group.dropup
               %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share
-- 
cgit v1.2.3


From 02357098113713b5ac5268ac19bf9443804c930e Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Fri, 29 Apr 2016 06:58:00 +0000
Subject: changed share and acknowledgement always visible

---
 views/layout.haml | 59 +++++++++++++++++++++++--------------------------------
 views/style.scss  | 18 +++++++++--------
 2 files changed, 35 insertions(+), 42 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 5965ee1..43e1233 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -32,11 +32,22 @@
           %h1.media-heading
             %small
               %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar
-          %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version
 
     %div.container-fluid
-      Problems, bugs, ideas for improvements ? Please report at our
-      %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
+      %topline
+        Problems, bugs, ideas for improvements ? Please report at our
+        %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker.
+        |
+        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version
+        |
+        %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
+          %img.share{:src=>"/images/Twitter.png"}
+        %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
+          %img.share{:src=>"/images/Google+.png"}
+        %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
+          %img.share{:src=>"/images/LinkedIn.png"}
+        %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
+          %img.share{:src=>"/images/Facebook.png"}
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -56,41 +67,21 @@
     %footer.footer
       %div.container-fluid
         %div.row
-          %div.col-md-8
+          %div.col-md-12
             %p.text-muted
               &copy; 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
-          %div.col-md-4
-            %button.btn.btn-default{:type=>"button", :data=>{:toggle=>"modal", :target=>"#acknowledgements"}} acknowledgements
-            %div.modal.fade{:id=>"acknowledgements", :role=>"dialog"}
-              %div.modal-dialog
-                %div.modal-content
-                  %div.modal-header
-                    %button{:type=>"button", :class=>"close", :data=>{:dismiss=>"modal"}}
-                      &times;
-                    %h4.modal-title Financial support:
-                  %div.modal-body
-                    %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
-                      %img{:src=>"/images/bfr_logo.gif"}
-                    %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
-                      %img{:src=>"/images/ot_logo.png"}
-                    %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
-                      %img{:src=>"/images/enm_logo.png"}
-                    %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
-                      %img{:src=>"/images/nestec.jpg"}
+          %supporters.col-md-12
+            %p Financial support:
+            %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
+              %img{:src=>"/images/bfr_logo.gif"}
+            %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
+              %img{:src=>"/images/ot_logo.png"}
+            %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
+              %img{:src=>"/images/enm_logo.png"}
+            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
+              %img{:src=>"/images/nestec.jpg"}
     
-            %div.btn-group.dropup
-              %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share
-              %ul.dropdown-menu{:class=>"share-buttons"}
-                %li
-                  %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
-                    %img{:src=>"/images/Twitter.png"}
-                %li
-                  %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
-                    %img{:src=>"/images/Google+.png"}
-                %li
-                  %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
-                    %img{:src=>"/images/LinkedIn.png"}
 
     #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
       %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
diff --git a/views/style.scss b/views/style.scss
index 77c7c4e..49e03ab 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -56,13 +56,15 @@ ul.share-buttons{
   display:inline-block;
   width:98.5%;
 }
-.footer .modal img{
-  width: 250px;
-  padding: 1em;
+.share{
+  width: 30px;
+  padding-right: 5px;
 }
-footer button{
-  padding-bottom: 1em !important;
-}
-.dropdown-menu img{
-  margin-left: 0.7em;
+supporters{
+  background-color: white;
+
+  img{
+    width: 200px;
+    margin-right: 1em;
+  }
 }
-- 
cgit v1.2.3


From 45dcce0598ec31389991c9e67be2683a8dfcc354 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Tue, 3 May 2016 08:44:30 +0000
Subject: final header adjustments

---
 views/layout.haml | 35 +++++++++++++++++++++--------------
 1 file changed, 21 insertions(+), 14 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 43e1233..13f351c 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -27,7 +27,7 @@
             %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
           %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
-            lazar Toxicity Predictions
+            lazar toxicity predictions
         %div.col-md-2
           %h1.media-heading
             %small
@@ -35,19 +35,26 @@
 
     %div.container-fluid
       %topline
-        Problems, bugs, ideas for improvements ? Please report at our
-        %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker.
-        |
-        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version
-        |
-        %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
-          %img.share{:src=>"/images/Twitter.png"}
-        %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
-          %img.share{:src=>"/images/Google+.png"}
-        %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
-          %img.share{:src=>"/images/LinkedIn.png"}
-        %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
-          %img.share{:src=>"/images/Facebook.png"}
+        %div.row
+          %div.col-md-8
+            Problems, bugs, ideas for improvements ? Please report at our
+            %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker.
+            or send us an email:
+            %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
+              %img.share{:src=>"/images/Email.png"}
+          %div.col-md-2
+          %div.col-md-2
+            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
+              %img.share{:src=>"/images/Twitter.png"}
+            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
+              %img.share{:src=>"/images/Google+.png"}
+            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
+              %img.share{:src=>"/images/LinkedIn.png"}
+            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
+              %img.share{:src=>"/images/Facebook.png"}
+        %div.row
+        Previous version:
+        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
-- 
cgit v1.2.3


From 769f704a2b4e2d83256f580317ed8c0b48cc4f45 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Wed, 8 Jun 2016 13:47:51 +0000
Subject: bumped version; added version to GUI

---
 views/layout.haml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'views')

diff --git a/views/layout.haml b/views/layout.haml
index 13f351c..a40b68c 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -38,10 +38,11 @@
         %div.row
           %div.col-md-8
             Problems, bugs, ideas for improvements ? Please report at our
-            %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker.
-            or send us an email:
+            %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker
+            or send us an email
             %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"}
               %img.share{:src=>"/images/Email.png"}
+            (version #{@version}).
           %div.col-md-2
           %div.col-md-2
             %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
-- 
cgit v1.2.3


From f86c084311282036ffa7b4588c0fa0d5b59af95b Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 24 Nov 2016 16:03:09 +0000
Subject: several fixes; works with lazar tree
 e111369ce5564f159b3f5f85c92afdd22352eaa1

---
 views/details.haml       |   2 +-
 views/layout.haml        |  18 ++++---
 views/license.haml       |   1 +
 views/model_details.haml | 134 +++++++++++++++++++++++++++--------------------
 views/neighbors.haml     |  13 +++--
 views/predict.haml       |   1 +
 views/prediction.haml    |  35 ++++++++-----
 views/style.scss         |  14 +++--
 views/validation.haml    |  16 ------
 9 files changed, 127 insertions(+), 107 deletions(-)
 create mode 100644 views/license.haml
 delete mode 100644 views/validation.haml

(limited to 'views')

diff --git a/views/details.haml b/views/details.haml
index 8a57440..bb8250d 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -19,6 +19,6 @@
   %hr
   %p{:style=>"padding-left:0.5em;"}
     / pubchem link
-    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across 
+    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across 
     %i (experimental)
   %br
diff --git a/views/layout.haml b/views/layout.haml
index a40b68c..dddf854 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -15,7 +15,7 @@
     %script{:src=>"/javascripts/bootstrap.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
     %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
-    %script{ :src=>"/javascripts/lazar-gui.js"}
+    %script{:src=>"/javascripts/lazar-gui.js"}
   %body
     %noscript
       %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
@@ -26,7 +26,7 @@
           %a{:href=> to("/predict")}
             %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"}
         %div.col-md-8
-          %h1.media-heading{:style=>"margin: 0 0 0 2em;"}
+          %h1.media-heading
             lazar toxicity predictions
         %div.col-md-2
           %h1.media-heading
@@ -55,7 +55,7 @@
               %img.share{:src=>"/images/Facebook.png"}
         %div.row
         Previous version:
-        %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old
+        %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old
       :javascript
         $(document).ready(function(){
           $("#back-top").hide();
@@ -79,15 +79,17 @@
             %p.text-muted
               &copy; 
               %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+              |
+              %a{:href => to("/license"), :rel => "external"} GPL3 License
           %supporters.col-md-12
-            %p Financial support:
-            %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"}
+            %p Financial support by
+            %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"}
               %img{:src=>"/images/bfr_logo.gif"}
-            %a{:href=>"http://www.opentox.org/", :target=>"_blank"}
+            %a{:href=>"http://www.opentox.org/", :rel=>"external"}
               %img{:src=>"/images/ot_logo.png"}
-            %a{:href=>"https://enanomapper.net/", :target=>"_blank"}
+            %a{:href=>"https://enanomapper.net/", :rel=>"external"}
               %img{:src=>"/images/enm_logo.png"}
-            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"}
+            %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"}
               %img{:src=>"/images/nestec.jpg"}
     
 
diff --git a/views/license.haml b/views/license.haml
new file mode 100644
index 0000000..2813220
--- /dev/null
+++ b/views/license.haml
@@ -0,0 +1 @@
+= @license
diff --git a/views/model_details.haml b/views/model_details.haml
index 1be75e7..7646471 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -1,26 +1,39 @@
 %b Model:
 %br
 Source:
-%a{:href=>model.source, :target=>"external"}
+%a{:href=>model.source, :rel=>"external"}
   = model.source
 %br
 - model.classification? ? type = "Classification" : type = "Regression"
 = "Type:\t"
 = type
 %br
-- training_dataset = OpenTox::Dataset.find model.training_dataset.id
+- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id
 = "Training compounds:\t"
 = training_dataset.compounds.size
-
+%br
+%b Algorithms:
+%br
+Similarity:
+%a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"}
+  = model.model.algorithms["similarity"]["method"]
+= ", min: #{model.model.algorithms["similarity"]["min"]}"
+%br
+Prediction:
+%a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+  = model.model.algorithms["prediction"]["method"]
+%br
+Descriptors:
+= model.model.algorithms["descriptors"]["method"]+","
+= model.model.algorithms["descriptors"]["type"]
 %p
 - if type == "Classification"
   %b Independent crossvalidations:
 - else
   %b Independent crossvalidations (-log10 transformed):
 %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"}
-  - model.crossvalidations.each do |crossvalidation|
+  - crossvalidations.each do |cv|
     %span.col-xs-4.col-sm-4.col-md-4.col-lg-4
-      - cv = OpenTox::CrossValidation.find crossvalidation.id
       = "Num folds:\t"
       = cv.folds
       %br
@@ -34,76 +47,81 @@ Source:
         = "Accuracy:\t"
         = cv.accuracy.round(3) if cv.accuracy
         %br
+        = "Weighted accuracy:\t"
+        = cv.weighted_accuracy.round(3) if cv.weighted_accuracy
+        %br
         = "True positive rate:\t"
-        = cv.true_rate["active"].round(3) if cv.true_rate["active"]
+        = cv.true_rate["active"].round(3) if cv.true_rate
         %br
         = "True negative rate:\t"
-        = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"]
+        = cv.true_rate["inactive"].round(3) if cv.true_rate
         %br 
         = "Positive predictive value:\t"
-        = cv.predictivity["active"].round(3) if cv.predictivity["active"]
+        = cv.predictivity["active"].round(3) if cv.predictivity
         %br
         = "Negative predictive value:\t"
-        = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"]
+        = cv.predictivity["inactive"].round(3) if cv.predictivity
         %p
-        %b Confusion Matrix:
-        %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
-          %tbody
-            %tr
-              %td
-              %td
-              %td 
-                %b actual
-              %td
-              %td
-            %tr
-              %td
-              %td
-              %td active
-              %td inactive
-              -#%td total
-            %tr
-              %td 
-                %b predicted
-              %td active
-              %td 
-                =cv.confusion_matrix[0][0]
-              %td 
-                =cv.confusion_matrix[0][1]
-              -#%td 
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
-            %tr
-              %td
-              %td inactive
-              %td 
-                =cv.confusion_matrix[1][0]
-              %td 
-                =cv.confusion_matrix[1][1]
-              -#%td 
-                =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
-            -#%tr
-              %td
-              %td total
-              %td
-                =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
-              %td
-                =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
-              %td
-                -#= "Confusion Matrix:\t"
-                -#= cv.confusion_matrix
+        - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx|
+          %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix")
+          %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
+            %tbody
+              %tr
+                %td
+                %td
+                %td 
+                  %b actual
+                %td
+                %td
+              %tr
+                %td
+                %td
+                %td active
+                %td inactive
+                -#%td total
+              %tr
+                %td 
+                  %b predicted
+                %td active
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][0].round(3) : cv.send(matrix)[0][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[0][1].round(3) : cv.send(matrix)[0][1])
+                -#%td 
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
+              %tr
+                %td
+                %td inactive
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][0].round(3) : cv.send(matrix)[1][0])
+                %td 
+                  =( idx == 1 ? cv.send(matrix)[1][1].round(3) : cv.send(matrix)[1][1])
+                -#%td 
+                  =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
+              -#%tr
+                %td
+                %td total
+                %td
+                  =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
+                %td
+                  =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
+                %td
+                  -#= "Confusion Matrix:\t"
+                  -#= cv.confusion_matrix
+              %br
         %br
         /= "Confidence plot:"
         /%p.plot
         /  %img{:src=>"confp#{cv.id}.svg"}
       - if model.regression?
         %br
-        = "Root mean squared error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
         = cv.rmse.round(3) if cv.rmse
         %br
-        = "Mean absolute error:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE:
         = cv.mae.round(3) if cv.mae
         %br 
-        = "R square:\t"
+        %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
         = cv.r_squared.round(3) if cv.r_squared
         %br
         /= "Confidence plot:"
@@ -113,5 +131,5 @@ Source:
         /= "Correlation plot"
         /%p.plot
         /  %img{:src=>"/corrp#{cv.id}.svg"}
-        
+          
 %br
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 096e432..d9f2796 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -79,20 +79,19 @@
                 - prediction[:neighbors].uniq.each_with_index do |neighbor,count|
                   %tr
                     / Compound
-                    - c = Compound.find(neighbor["_id"])
+                    - c = Compound.find(neighbor)
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
                       /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}}
                       %p= c.svg
                       %p= c.smiles
-                    - mw = c.molecular_weight
-                    / Measured Activity = compound.features
+                    / Measured Activity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
-                      - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten
-                      = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>")
+                      = (type == "Regression" ? "#{neighbor[:measurement].delog10}" + " (#{unit})" : neighbor[:measurement])
+                      %br
+                      = "#{c.mmol_to_mg(neighbor[:measurement].delog10)}" + " (#{(unit =~ /\b(mol\/L)\b/) ? "mg/L" : "mg/kg_bw/day"})" if type == "Regression"
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
-                      = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset."
+                      = neighbor[:similarity].round(3)
 
           - else
             %span.btn.btn-default.disabled
diff --git a/views/predict.haml b/views/predict.haml
index 010ed12..8ae5684 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -162,6 +162,7 @@
                     document.getElementById("details#{model.id}").appendChild(details);
                     $(button).show();
                     $(image).hide();
+                    addExternalLinks();
                   });
                 }
               }
diff --git a/views/prediction.haml b/views/prediction.haml
index 0f3d57b..1aefe06 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,7 +18,6 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
-          - mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -29,17 +28,20 @@
               %b{:class => "title"}
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
               %p
-              - if prediction[:confidence] == "measured"
+              - if prediction[:warning] =~ /\b(identical)\b/i
                 - @dbhit[i] = true
                 %p
+                /TODO combine with regular view, if prediction value is present
                 %b Measured activity:
                 - p prediction[:value]
                 - if prediction[:value].is_a?(Array)
-                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
+                  = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ")
                 - else
-                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                  = (type == "Regression") ? "#{prediction[:value]} (#{unit}), #{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
                 %p
                   %b Compound is part of the training dataset
+                  / warning popover
+                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}}
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -47,23 +49,30 @@
                 = type
                 %br
                 %b Prediction:
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
                 / prediction popover
                 %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}}
                 %br
+                = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
+                / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF.
+                %br
                 - if type == "Regression"
                   %b 95% Prediction interval:
-                  - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)}
-                  %br
-                  = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"
+                  - interval = (prediction[:prediction_interval].nil? ? ["- -","- -"] : prediction[:prediction_interval])
                   / prediction intervall popover
                   %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}}
+                  %br
+                  = "#{interval[0].delog10} - #{interval[1].delog10} (#{unit})"
+                  %br
+                  = "#{@compound.mmol_to_mg(interval[0].delog10)} - #{@compound.mmol_to_mg(interval[1].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
                 - else
-                  %b Confidence:
-                  = prediction[:confidence].round(2) unless prediction[:confidence].nil?
-                  / confidence popover
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
+                  %b Probability:
+                  - unless prediction[:probabilities].nil?
+                    %br
+                    = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}"
+                    %br
+                    = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}"
+                  / probability popover
+                  -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
                 %p
                 /TODO add tooltip for significant ftagments and descriptors
                 / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
diff --git a/views/style.scss b/views/style.scss
index 49e03ab..2c84781 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -51,10 +51,12 @@ ul.share-buttons{
   padding: 0 2px 1px 2px !important;
 }
 .page-header{
-  margin:20px 0 20px;
-  text-align:justify;
+  background-color: #fff;
+  padding:20px 0 20px 0;
+  margin: 0;
+  text-align:center;
   display:inline-block;
-  width:98.5%;
+  width:100%;
 }
 .share{
   width: 30px;
@@ -62,9 +64,13 @@ ul.share-buttons{
 }
 supporters{
   background-color: white;
-
+  text-align:center;
   img{
     width: 200px;
     margin-right: 1em;
   }
 }
+
+.footer{
+  margin-top:3em;
+}
diff --git a/views/validation.haml b/views/validation.haml
deleted file mode 100644
index fd63ea6..0000000
--- a/views/validation.haml
+++ /dev/null
@@ -1,16 +0,0 @@
-- case @model_type
-- when "classification"
-  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numCorrect"] + @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numIncorrect"]
-  %p= "Number of predictions: #{prediction}"
-  - percent = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#percentCorrect"]
-  %p= "Correct predictions: #{percent.round(2)} %"
-- when "regression"
-  - prediction = @cv.metadata["http://www.opentox.org/api/1.2#numInstances"].to_i - @cv.metadata["http://www.opentox.org/api/1.2#numUnpredicted"].to_i
-  %p= "Number of predictions: #{prediction}"
-  - rSquare = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rSquare"]
-  %p= "R-squared: #{rSquare.round(2)} %"
-  - rootMeanSquaredError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rootMeanSquaredError"]
-  %p= "Root Mean Square Error: #{rootMeanSquaredError.round(2)} %"
-  - meanAbsoluteError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#meanAbsoluteError"]
-  %p= "Mean Absolute Error: #{meanAbsoluteError.round(2)} %"
-
-- 
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